Marker enrichment and construction of haplotype-specific BAC contigs for the polyembryony genomic region in Citrus

Nakano, Michiharu; Shimizu, Tokurou; Fujii, Hiroshi; Shimada, Takehiko; Endo, Tetsuro; Nesumi, Hirohisa; Kuniga, Takeshi; Omura, Mitsuo

doi:10.1270/jsbbs.58.375

Cited by 18 publications

(5 citation statements)

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“…Through a continuous effort of DNA marker landing and BAC walking with DNA sequencing of Satsuma BAC clones, Nakano with colleagues enriched CAPS or SNP markers surrounding the polyembryony locus. They evaluated haplotype structure by means of these markers and constructed haplotype-specific BAC contigs that cover the genomic region of the polyembryony locus (Nakano et al 2008a). Comparative mapping among five cross populations with the developed DNA markers flanking the polyembryony locus demonstrated similar lineage of these markers, and it suggested that a region flanking the polyembryony locus could be conserved among a wide variety of polyembryonic citrus plants.…”

Section: Fine Mapping Of a Locus Involved In Polyembryonymentioning

confidence: 99%

Citrus genomics

Gmitter

Chen

Machado³

et al. 2012

Tree Genetics & Genomes

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103

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Citrus fruits (sweet orange, mandarin, pummelo, grapefruit, lemon, lime and assorted hybrids) are among the most widely grown and economically important fruit tree crops in the world. As fresh fruit, they are an important and nutrient dense food source for human diets; as processed juice products, primarily sweet orange juice, they represent a globally traded commodity. To support genetic improvement efforts for this important crop, the international citrus genetics community has collaborated with international sequencing centers in the development of freely available genomic resources, some of which are described herein. Most notable, two full-length annotated genome assemblies have been produced and made available to the global research community. The first genome, based exclusively on Sanger sequencing, is from a haploid plant derived from 'Clementine' mandarin, to serve as the reference genome for citrus. A second genome assembly was produced from the sweet orange clone 'Ridge Pineapple', this was done primarily with 454 technology. Extensive EST datasets and a number of microarray platforms for exploring the transcriptomic responses of citrus species and hybrids to a wide range of conditions have been shared, to support exploitation and utilization of genome sequence information. As many researchers in the citrus genomics community are also actively engaged in genetic improvement programs, there has been a natural integration of improvement efforts with the rapidly evolving genomic tools. Examples described below include work designed to better understand the control of gene expression in citrus polyploids, which are being used in development of seedless triploid selections or as rootstocks; unraveling the molecular mechanisms of host-pathogen interactions to devise novel genetic strategies to overcome a multitude of devastating diseases that currently threaten citrus production globally; and the mining of SSR and SNP markers for linkage studies to enable marker-assisted parental selection and breeding strategies, illustrated bywork on two citrus traits, nucellar embryony and juvenility, which significantly impact breeding approaches. Citrus genome resources are available through publicly available web portals, through the USDOEJGI (phytozome.net) and Tree Fruit Genome Database Resources (tfGDR, citrusgenomedb.org). Work is continuing to expand and improve the citrus genome sequence resources and tools, to enable application of sequence-derived knowledge in improving citrus plants and to managing better their interactions with biotic and abiotic factors. (Résumé d'auteur

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Section: Fine Mapping Of a Locus Involved In Polyembryonymentioning

confidence: 99%

Citrus genomics

Gmitter

Chen

Machado³

et al. 2012

Tree Genetics & Genomes

Self Cite

103

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“…It is conceivable that a single or a few genes are involved in the somatic embryogenesis and several molecular markers linked to a polyembryonic locus controlling embryonic type (mono/polyembryony) have been developed [ 11 , 17 , 29 ]. In our previous studies [ 29 , 30 ], a major polyembryonic locus was located on linkage group 1 of the mandarin standard genetic map (AGI map) [ 36 ] and scaffold 1 of the clementine mandarin ( C. clementina hort ex. Tanaka) genome sequence [ 42 ].…”

Section: Introductionmentioning

confidence: 99%

MITE insertion-dependent expression of CitRKD1 with a RWP-RK domain regulates somatic embryogenesis in citrus nucellar tissues

et al. 2018

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BackgroundSomatic embryogenesis in nucellar tissues is widely recognized to induce polyembryony in major citrus varieties such as sweet oranges, satsuma mandarins and lemons. This capability for apomixis is attractive in agricultural production systems using hybrid seeds, and many studies have been performed to elucidate the molecular mechanisms of various types of apomixis. To identify the gene responsible for somatic embryogenesis in citrus, a custom oligo-DNA microarray including predicted genes in the citrus polyembryonic locus was used to compare the expression profiles in reproductive tissues between monoembryonic and polyembryonic varieties. The full length of CitRKD1, which was identified as a candidate gene responsible for citrus somatic embryogenesis, was isolated from satsuma mandarin and its molecular function was investigated using transgenic ‘Hamlin’ sweet orange by antisense-overexpression.ResultsThe candidate gene CitRKD1, predominantly transcribed in reproductive tissues of polyembryonic varieties, is a member of the plant RWP-RK domain-containing protein. CitRKD1 of satsuma mandarin comprised two alleles (CitRKD1-mg1 and CitRKD1-mg2) at the polyembryonic locus controlling embryonic type (mono/polyembryony) that were structurally divided into two types with or without a miniature inverted-repeat transposable element (MITE)-like insertion in the upstream region. CitRKD1-mg2 with the MITE insertion was the predominant transcript in flowers and young fruits where somatic embryogenesis of nucellar cells occurred. Loss of CitRKD1 function by antisense-overexpression abolished somatic embryogenesis in transgenic sweet orange and the transgenic T1 plants were confirmed to derive from zygotic embryos produced by self-pollination by DNA diagnosis. Genotyping PCR analysis of 95 citrus traditional and breeding varieties revealed that the CitRKD1 allele with the MITE insertion (polyembryonic allele) was dominant and major citrus varieties with the polyembryonic allele produced polyembryonic seeds.ConclusionCitRKD1 at the polyembryonic locus plays a principal role in regulating citrus somatic embryogenesis. CitRKD1 comprised multiple alleles that were divided into two types, polyembryonic alleles with a MITE insertion in the upstream region and monoembryonic alleles without it. CitRKD1 was transcribed in reproductive tissues of polyembryonic varieties with the polyembryonic allele. The MITE insertion in the upstream region of CitRKD1 might be involved in regulating the transcription of CitRKD1.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1369-3) contains supplementary material, which is available to authorized users.

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“…In earlier reports, it has been proposed that NE is controlled by either a single, two, or multiple loci ( Iwamasa et al , 1967 ; García et al , 1999 ; Hong et al , 2001 a ). In later studies, molecular markers related to NE were identified ( Nakano et al , 2008 a , b ; Kepiro and Roose, 2010 ). The most recent report on genetics of citrus NE suggested that the candidate genomic region for the polyembryony locus is represented by an approximately 380-kb fragment ( Nakano et al , 2012 ).…”

Section: Introductionmentioning

confidence: 99%